10 Pseudobulk
Run reintegration after cleaning
10.1 REINTEGRATION
The integrated scRNAseq dataset of all brain cell populations was subsetted to retain those cells no subsetted out by the “expert committee”.
10.2 PCA
PC details
PC1 captures a strong myelination axis, with high loadings for oligodendrocyte and myelin-related genes (Plp1, Mbp, Mag, Mal, Car2, Cryab) and opposite contributions from astrocytic (Ptgds, Enpp2, Edil3) and microglial (Hexb, C1qa, Ctss, Cst3) markers.
PC2 reflects a neuron–astrocyte interaction gradient, driven by the astrocytic ECM regulator Sparcl1 on one pole and the neuronal signaling gene Plcb1 on the other.
PC3 highlights synaptic connectivity and neurotransmission, with neuronal adhesion and plasticity genes (Nrxn1, Ntm, Lsamp, Ctnnd2, Adgrb3, Ntrk2) and the inhibitory receptor Gabrb1 loading strongly, balanced by astrocytic transporters (Slc1a2, Slc4a4) and Ptprz1. Together, these axes describe complementary layers of variance corresponding to myelination, glial–neuronal signaling, and synaptic specialization.
10.3 UMAP after reintegration
10.4 Pseudobulk
10.4.1 Astrocytes
| p_val | avg_log2FC | pct.1 | pct.2 | p_val_adj | |
|---|---|---|---|---|---|
| Wdr17 | 1.0e-07 | -0.6656742 | 1 | 1 | 0.0011904 |
| Lpar1 | 1.0e-07 | 0.5192552 | 1 | 1 | 0.0012595 |
| Dcc | 1.0e-07 | -0.6273549 | 1 | 1 | 0.0030505 |
| Wif1 | 7.0e-07 | 0.1848369 | 1 | 1 | 0.0159661 |
| Sorcs1 | 1.1e-06 | 0.3837130 | 1 | 1 | 0.0234440 |
| Tmsb4x | 1.8e-06 | 0.8196337 | 1 | 1 | 0.0383954 |
| Tenm2 | 2.2e-06 | 0.3594390 | 1 | 1 | 0.0476388 |
10.4.2 BAM
| p_val | avg_log2FC | pct.1 | pct.2 | p_val_adj | |
|---|---|---|---|---|---|
| Cxcl13 | 0e+00 | 1.9569000 | 1 | 0.333 | 0.0002040 |
| Wfdc17 | 2e-06 | -0.8501451 | 1 | 1.000 | 0.0435564 |
10.4.3 Choroid
| p_val | avg_log2FC | pct.1 | pct.2 | p_val_adj | |
|---|---|---|---|---|---|
| Rgs2 | 0 | 0.9370808 | 1 | 1 | 0.00068 |
10.4.4 Endothelial
| p_val | avg_log2FC | pct.1 | pct.2 | p_val_adj | |
|---|---|---|---|---|---|
| Gria1 | 1e-07 | 0.2876162 | 1 | 1 | 0.0014814 |
| Slc38a2 | 5e-07 | -0.3942290 | 1 | 1 | 0.0101714 |
10.4.5 Ependymal
| p_val | avg_log2FC | pct.1 | pct.2 | p_val_adj | |
|---|---|---|---|---|---|
| Mt3 | 1e-07 | -0.581966 | 1 | 1 | 0.0014678 |
10.4.6 Neurons
| p_val | avg_log2FC | pct.1 | pct.2 | p_val_adj | |
|---|---|---|---|---|---|
| Cldn5 | 0.0e+00 | 0.8740228 | 1.000 | 1.000 | 0.0000026 |
| Ly6c1 | 0.0e+00 | 0.8417682 | 1.000 | 1.000 | 0.0000039 |
| Hapln1 | 0.0e+00 | -1.0575334 | 0.667 | 1.000 | 0.0000206 |
| Slco1a4 | 0.0e+00 | 0.9098885 | 1.000 | 0.667 | 0.0000294 |
| Ptprb | 0.0e+00 | 0.7883225 | 1.000 | 0.667 | 0.0003976 |
| Vgf | 1.1e-06 | 0.8479086 | 1.000 | 1.000 | 0.0243259 |
| Ly6a | 1.6e-06 | 0.7068322 | 1.000 | 0.667 | 0.0353316 |
10.4.7 NPC
| p_val | avg_log2FC | pct.1 | pct.2 | p_val_adj | |
|---|---|---|---|---|---|
| Ikzf1 | 0.0e+00 | 1.0571115 | 1 | 1 | 0.0000004 |
| Runx1 | 0.0e+00 | 1.3537906 | 1 | 1 | 0.0000057 |
| Creg1 | 0.0e+00 | 1.0016099 | 1 | 1 | 0.0000301 |
| Gpr183 | 0.0e+00 | 1.1165005 | 1 | 1 | 0.0000624 |
| Adamts1 | 0.0e+00 | 0.9092272 | 1 | 1 | 0.0001537 |
| Inpp5d | 0.0e+00 | 1.1274030 | 1 | 1 | 0.0001906 |
| Zfp36 | 0.0e+00 | 1.0025476 | 1 | 1 | 0.0003610 |
| Lmo2 | 0.0e+00 | 0.9614975 | 1 | 1 | 0.0003979 |
| Lrmda | 0.0e+00 | 0.9927620 | 1 | 1 | 0.0009119 |
| Fth1 | 1.0e-07 | 0.7754402 | 1 | 1 | 0.0015168 |
| Sat1 | 1.0e-07 | 1.1250506 | 1 | 1 | 0.0016771 |
| Lpcat2 | 1.0e-07 | 0.9794508 | 1 | 1 | 0.0017612 |
| Unc93b1 | 1.0e-07 | 1.1107730 | 1 | 1 | 0.0018391 |
| Nfkbia | 1.0e-07 | 0.8980613 | 1 | 1 | 0.0019855 |
| Tmem119 | 1.0e-07 | 0.8763570 | 1 | 1 | 0.0020384 |
| Ptprc | 2.0e-07 | 0.9292133 | 1 | 1 | 0.0042320 |
| Lgals9 | 3.0e-07 | 0.7196859 | 1 | 1 | 0.0058081 |
| Adap2 | 3.0e-07 | 0.8139424 | 1 | 1 | 0.0071801 |
| P2ry12 | 6.0e-07 | 1.0277527 | 1 | 1 | 0.0118773 |
| Cd83 | 7.0e-07 | 0.9920499 | 1 | 1 | 0.0145304 |
| Itgam | 7.0e-07 | 1.0216380 | 1 | 1 | 0.0145724 |
| Abca9 | 8.0e-07 | 0.8031022 | 1 | 1 | 0.0174620 |
| Rnase4 | 8.0e-07 | 0.8590141 | 1 | 1 | 0.0179884 |
| Ly6e | 8.0e-07 | 0.8554275 | 1 | 1 | 0.0180234 |
| H2-T23 | 1.6e-06 | 0.7770506 | 1 | 1 | 0.0350168 |
| Selplg | 1.6e-06 | 0.7707752 | 1 | 1 | 0.0351740 |
| Lyn | 1.8e-06 | 0.9601579 | 1 | 1 | 0.0397079 |
| St3gal6 | 2.1e-06 | 0.8886279 | 1 | 1 | 0.0453242 |
10.4.8 Oligodendrocytes
| p_val | avg_log2FC | pct.1 | pct.2 | p_val_adj | |
|---|---|---|---|---|---|
| Ms4a6b | 5.0e-07 | 0.0686229 | 1 | 1 | 0.0096832 |
| C1qa | 8.0e-07 | 0.4272693 | 1 | 1 | 0.0167962 |
| Shoc2 | 9.0e-07 | -0.2455762 | 1 | 1 | 0.0196189 |
| Ctss | 1.2e-06 | 0.4387682 | 1 | 1 | 0.0254450 |
| mt-Atp8 | 1.3e-06 | -0.3642960 | 1 | 1 | 0.0273779 |
| mt-Nd4l | 2.0e-06 | -0.4666682 | 1 | 1 | 0.0426910 |
10.4.9 OPC
| p_val | avg_log2FC | pct.1 | pct.2 | p_val_adj | |
|---|---|---|---|---|---|
| Hpgd | 5e-07 | -1.446021 | 1 | 1 | 0.0109219 |
10.4.10 T-cell
| p_val | avg_log2FC | pct.1 | pct.2 | p_val_adj | |
|---|---|---|---|---|---|
| Dscam | 4e-07 | 0.8264654 | 1 | 1 | 0.008977 |
10.4.11 VMC
| p_val | avg_log2FC | pct.1 | pct.2 | p_val_adj | |
|---|---|---|---|---|---|
| Rbp4 | 0 | 1.454712 | 1 | 0.667 | 0.0003589 |